Biomolecular engineering of virus-like particles aided by computational chemistry methods

Mechanisms of Virus Assembly

(2015) Jason D. Perlmutter et al.   Annual Review of Physical Chemistry

Improved virus purification processes for vaccines and gene therapy

(2015) Piergiuseppe Nestola et al.   BIOTECHNOLOGY AND BIOENGINEERING

Assembly engineering: Materials design for the 21st century (2013 P.V. Danckwerts lecture)

(2015) Sharon C. Glotzer   CHEMICAL ENGINEERING SCIENCE

Designing soft nanomaterials via the self assembly of functionalized icosahedral viral capsid nanoparticles

(2015) Vidyalakshmi Chockalingam Muthukumar et al.   JOURNAL OF MATERIALS RESEARCH

Production and applications of engineered viral capsids

(2014) Jeff Glasgow et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The Hepatitis B Virus Core Protein Intradimer Interface Modulates Capsid Assembly and Stability

(2014) Lisa Selzer et al.   BIOCHEMISTRY

Applying Molecular Crowding Models to Simulations of Virus Capsid Assembly In Vitro

(2014) Gregory R. Smith et al.   BIOPHYSICAL JOURNAL

GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting

(2014) John E. Stone et al.   FARADAY DISCUSSIONS

Using Markov state models to study self-assembly

(2014) Matthew R. Perkett et al.   JOURNAL OF CHEMICAL PHYSICS

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

(2014) Y. Andoh et al.   JOURNAL OF CHEMICAL PHYSICS

Pathways for Virus Assembly around Nucleic Acids

(2014) Jason D. Perlmutter et al.   JOURNAL OF MOLECULAR BIOLOGY

Detection of Late Intermediates in Virus Capsid Assembly by Charge Detection Mass Spectrometry

(2014) Elizabeth E. Pierson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Biomimetic Design of Affinity Peptide Ligand for Capsomere of Virus-Like Particle

(2014) Yanying Li et al.   LANGMUIR

Biomimetic Design of Platelet Adhesion Inhibitors to Block Integrin α2β1-Collagen Interactions: II. Inhibitor Library, Screening, and Experimental Validation

(2014) Lin Zhang et al.   LANGMUIR

Biomimetic Design of Platelet Adhesion Inhibitors to Block Integrin α2β1-Collagen Interactions: I. Construction of an Affinity Binding Model

(2014) Lin Zhang et al.   LANGMUIR

Functionalization of protein-based nanocages for drug delivery applications

(2014) Lise Schoonen et al.   Nanoscale

Accurate design of co-assembling multi-component protein nanomaterials

(2014) Neil P. King et al.   NATURE

Computational self-assembly of a one-component icosahedral quasicrystal

(2014) Michael Engel et al.   NATURE MATERIALS

RNA topology remolds electrostatic stabilization of viruses

(2014) Gonca Erdemci-Tandogan et al.   PHYSICAL REVIEW E

Differentiating Coeliac Disease from Irritable Bowel Syndrome by Urinary Volatile Organic Compound Analysis – A Pilot Study

(2014) Ramesh P. Arasaradnam et al.   PLoS One

Encapsidated hepatitis B virus reverse transcriptase is poised on an ordered RNA lattice

(2014) J. C.-Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scaffold Properties Are a Key Determinant of the Size and Shape of Self-Assembled Virus-Derived Particles

(2013) Stanislav Kler et al.   ACS Chemical Biology

Hepatitis Virus Capsid Polymorph Stability Depends on Encapsulated Cargo Size

(2013) Li He et al.   ACS Nano

To Build a Virus on a Nucleic Acid Substrate

(2013) Adam Zlotnick et al.   BIOPHYSICAL JOURNAL

Bioengineering virus-like particles as vaccines

(2013) Linda H.L. Lua et al.   BIOTECHNOLOGY AND BIOENGINEERING

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Virus-like particles: the future of microbial factories and cell-free systems as platforms for vaccine development

(2013) William A Rodríguez-Limas et al.   CURRENT OPINION IN BIOTECHNOLOGY

Biomolecular scaffolds for enhanced signaling and catalytic efficiency

(2013) Rebecca Chen et al.   CURRENT OPINION IN BIOTECHNOLOGY

SV40 virus-like particles as an effective delivery system and its application to a vaccine carrier

(2013) Masaaki Kawano et al.   Expert Review of Vaccines

Impact of the topology of viral RNAs on their encapsulation by virus coat proteins

(2013) Paul van der Schoot et al.   JOURNAL OF BIOLOGICAL PHYSICS

Structure-based design and experimental engineering of a plant virus nanoparticle for the presentation of immunogenic epitopes and as a drug carrier

(2013) Caterina Arcangeli et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Production and biomedical applications of virus-like particles derived from polyomaviruses

(2013) Erik A. Teunissen et al.   JOURNAL OF CONTROLLED RELEASE

The Assembly Pathway of an Icosahedral Single-Stranded RNA Virus Depends on the Strength of Inter-Subunit Attractions

(2013) Rees F. Garmann et al.   JOURNAL OF MOLECULAR BIOLOGY

Site-Specific Structural Variations Accompanying Tubular Assembly of the HIV-1 Capsid Protein

(2013) Marvin J. Bayro et al.   JOURNAL OF MOLECULAR BIOLOGY

Dynamics of Self-assembly of Model Viral Capsids in the Presence of a Fluctuating Membrane

(2013) Richard Matthews et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Energetics in the Capsomere of Virus-Like Particle Revealed by Molecular Dynamics Simulations

(2013) Lin Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Epitope Fluctuations in the Human Papillomavirus Are Under Dynamic Allosteric Control: A Computational Evaluation of a New Vaccine Design Strategy

(2013) Abhishek Singharoy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Virus-like particle formulation optimization by miniaturized high-throughput screening

(2013) Johannes Mohr et al.   METHODS

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

(2013) Gongpu Zhao et al.   NATURE

Virus-like particle-based human vaccines: quality assessment based on structural and functional properties

(2013) Qinjian Zhao et al.   TRENDS IN BIOTECHNOLOGY

Sensitivity of immune response quality to influenza helix 190 antigen structure displayed on a modular virus-like particle

(2013) Melisa R. Anggraeni et al.   VACCINE

Epitope engineering and molecular metrics of immunogenicity: A computational approach to VLP-based vaccine design

(2013) Harshad Joshi et al.   VACCINE

Fine Tuning Inflammation at the Front Door: Macrophage Complement Receptor 3-mediates Phagocytosis and Immune Suppression for Francisella tularensis

(2013) Shipan Dai et al.   PLoS Pathogens

Viral genome structures are optimal for capsid assembly

(2013) Jason D Perlmutter et al.   eLife

Surveying Capsid Assembly Pathways through Simulation-Based Data Fitting

(2012) Lu Xie et al.   BIOPHYSICAL JOURNAL

Early Stages of the HIV-1 Capsid Protein Lattice Formation

(2012) John M.A. Grime et al.   BIOPHYSICAL JOURNAL

Vaccine process technology

(2012) Jessica O. Josefsberg et al.   BIOTECHNOLOGY AND BIOENGINEERING

Coarse-graining of multiprotein assemblies

(2012) Marissa G Saunders et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Langevin dynamics simulation of polymer-assisted virus-like assembly

(2012) J. P. Mahalik et al.   JOURNAL OF CHEMICAL PHYSICS

Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters

(2012) Abhishek Singharoy et al.   Journal of Chemical Theory and Computation

A Computationally Optimized Hemagglutinin Virus-Like Particle Vaccine Elicits Broadly Reactive Antibodies that Protect Nonhuman Primates from H5N1 Infection

(2012) Brendan M. Giles et al.   JOURNAL OF INFECTIOUS DISEASES

Unclosed HIV-1 Capsids Suggest a Curled Sheet Model of Assembly

(2012) Zhiheng Yu et al.   JOURNAL OF MOLECULAR BIOLOGY

Investigation of a predicted N-terminal amphipathic α-helix using atomistic molecular dynamics simulation of a complete prototype poliovirus virion

(2012) Jason A. Roberts et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

A Virus-Like Particle That Elicits Cross-Reactive Antibodies to the Conserved Stem of Influenza Virus Hemagglutinin

(2012) A. Schneemann et al.   JOURNAL OF VIROLOGY

Impact of charge variation on the encapsulation of nanoparticles by virus coat proteins

(2012) Hsiang-Ku Lin et al.   PHYSICAL BIOLOGY

Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles

(2012) D. C. Rapaport   PHYSICAL REVIEW E

Influence of Fluctuating Membranes on Self-Assembly of Patchy Colloids

(2012) Richard Matthews et al.   PHYSICAL REVIEW LETTERS

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

(2012) N. P. King et al.   SCIENCE

Predictive Self-Assembly of Polyhedra into Complex Structures

(2012) P. F. Damasceno et al.   SCIENCE

Virus scaffolds as enzyme nano-carriers

(2012) Daniela Cardinale et al.   TRENDS IN BIOTECHNOLOGY

Virus-like particles as a highly efficient vaccine platform: Diversity of targets and production systems and advances in clinical development

(2012) Natasha Kushnir et al.   VACCINE

Molecular dynamics simulation in virus research

(2012) Hirotaka Ode et al.   Frontiers in Microbiology

Simulated Self-Assembly of the HIV-1 Capsid: Protein Shape and Native Contacts Are Sufficient for Two-Dimensional Lattice Formation

(2011) Bo Chen et al.   BIOPHYSICAL JOURNAL

Synthesis and application of virus-based hybrid nanomaterials

(2011) Sang-Yup Lee et al.   BIOTECHNOLOGY AND BIOENGINEERING

Virus‑like particles as a vaccine delivery system: Myths and facts

(2011) Polly Roy et al.   Human vaccines & immunotherapeutics

Order parameters for macromolecules: Application to multiscale simulation

(2011) A. Singharoy et al.   JOURNAL OF CHEMICAL PHYSICS

Mechanisms of kinetic trapping in self-assembly and phase transformation

(2011) Michael F. Hagan et al.   JOURNAL OF CHEMICAL PHYSICS

Large-scale production and purification of VLP-based vaccines

(2011) Tiago Vicente et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Improvement of different vaccine delivery systems for cancer therapy

(2011) Azam Bolhassani et al.   Molecular Cancer

Atomic-level modelling of the HIV capsid

(2011) Owen Pornillos et al.   NATURE

Protein delivery using engineered virus-like particles

(2011) S. J. Kaczmarczyk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale simulation of microbe structure and dynamics

(2011) Harshad Joshi et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Templated self-assembly of patchy particles

(2011) Alexander J. Williamson et al.   Soft Matter

A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: A possible indicator of immunogenicity

(2011) Harshad Joshi et al.   VACCINE

Exploring the Paths of (Virus) Assembly

(2010) Paul Moisant et al.   BIOPHYSICAL JOURNAL

Mechanisms of Capsid Assembly around a Polymer

(2010) Aleksandr Kivenson et al.   BIOPHYSICAL JOURNAL

Multiscale Computer Simulation of the Immature HIV-1 Virion

(2010) Gary S. Ayton et al.   BIOPHYSICAL JOURNAL

Role of Protein Interactions in Defining HIV-1 Viral Capsid Shape and Stability: A Coarse-Grained Analysis

(2010) Vinod Krishna et al.   BIOPHYSICAL JOURNAL

Understanding the Concentration Dependence of Viral Capsid Assembly Kinetics—the Origin of the Lag Time and Identifying the Critical Nucleus Size

(2010) Michael F. Hagan et al.   BIOPHYSICAL JOURNAL

Modeling the competition between aggregation and self-assembly during virus-like particle processing

(2010) Yong Ding et al.   BIOTECHNOLOGY AND BIOENGINEERING

Virus-like particles in vaccine development

(2010) António Roldão et al.   Expert Review of Vaccines

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials

(2010) Luca Larini et al.   JOURNAL OF CHEMICAL PHYSICS

Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for En5hanced Presentation of HIV-1 gp41 Epitopes

(2010) Mauro Lapelosa et al.   JOURNAL OF MOLECULAR BIOLOGY

All-Atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling

(2010) Yinglong Miao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations

(2010) Stephen D. Hicks et al.   PHYSICAL REVIEW E

Thermodynamics of nanospheres encapsulated in virus capsids

(2010) Antonio Šiber et al.   PHYSICAL REVIEW E

Optimal architectures of elongated viruses

(2010) A. Luque et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virus assembly, allostery and antivirals

(2010) Adam Zlotnick et al.   TRENDS IN MICROBIOLOGY

Catalytic capsids: the art of confinement

(2010) Inge J. Minten et al.   Chemical Science

Elucidating the Mechanism behind Irreversible Deformation of Viral Capsids

(2009) Anton Arkhipov et al.   BIOPHYSICAL JOURNAL

Modeling the separation of macromolecules: A review of current computer simulation methods

(2009) Gary W. Slater et al.   ELECTROPHORESIS

A theory for viral capsid assembly around electrostatic cores

(2009) Michael F. Hagan   JOURNAL OF CHEMICAL PHYSICS

Monodisperse self-assembly in a model with protein-like interactions

(2009) Alex W. Wilber et al.   JOURNAL OF CHEMICAL PHYSICS

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

Invariant Polymorphism in Virus Capsid Assembly

(2009) Hung D. Nguyen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Virus assembly occurs following a pH- or Ca2+-triggered switch in the thermodynamic attraction between structural protein capsomeres

(2009) Y. P. Chuan et al.   Journal of the Royal Society Interface

Viruses and virus-like protein assemblies—Chemically programmable nanoscale building blocks

(2009) L. Andrew Lee et al.   Nano Research

Energy landscapes for shells assembled from pentagonal and hexagonal pyramids

(2009) Szilard N. Fejer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Nonequilibirum Assembly, Retroviruses, and Conical Structures

(2009) Artem Levandovsky et al.   PHYSICAL REVIEW LETTERS

Encapsulation of DNA and non-viral protein changes the structure of murine polyomavirus virus-like particles

(2008) D. I. Lipin et al.   ARCHIVES OF VIROLOGY

Size Regulation of ss-RNA Viruses

(2008) Roya Zandi et al.   BIOPHYSICAL JOURNAL

Pathway Complexity of Model Virus Capsid Assembly Systems

(2008) Navodit Misra et al.   Computational and Mathematical Methods in Medicine

In Silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes

(2008) Mauro Lapelosa et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure and dynamics of the anti-AMCV scFv(F8): Effects of selected mutations on the antigen combining site

(2008) Caterina Arcangeli et al.   JOURNAL OF STRUCTURAL BIOLOGY

Generalized Structural Polymorphism in Self-Assembled Viral Particles

(2008) Hung D. Nguyen et al.   NANO LETTERS

Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly

(2008) Oren M. Elrad et al.   NANO LETTERS

VIPERdb2: an enhanced and web API enabled relational database for structural virology

(2008) M. Carrillo-Tripp et al.   NUCLEIC ACIDS RESEARCH

Controlling viral capsid assembly with templating

(2008) Michael F. Hagan   PHYSICAL REVIEW E

Role of Reversibility in Viral Capsid Growth: A Paradigm for Self-Assembly

(2008) D. C. Rapaport   PHYSICAL REVIEW LETTERS

The role of collective motion in examples of coarsening and self-assembly

(2008) Stephen Whitelam et al.   Soft Matter

Exploring the Parameter Space of Complex Self-Assembly through Virus Capsid Models

(2007) Blake Sweeney et al.   BIOPHYSICAL JOURNAL

Packaging of a Polymer by a Viral Capsid: The Interplay between Polymer Length and Capsid Size

(2007) Yufang Hu et al.   BIOPHYSICAL JOURNAL

A reaction landscape identifies the intermediates critical for self-assembly of virus capsids and other polyhedral structures

(2005) Dan Endres et al.   PROTEIN SCIENCE